粗首馬口鱲以高屏溪為界的南北遺傳分化機制

Abstract

粗首馬口鱲（Opsariichthys pachycephalus）是屬於鲴科（Xenocyprididae）的初級淡水魚類，主要分布於臺灣西部河川。以高屏溪為界其粒線體基因以及同功酶基因型能分為南北兩個族群，並且過去的研究中以cytb 確認到有高屏溪以北的個體被放流至南部的狀況。目前粗首馬口鱲缺少對核基因的族群研究，因此將透過全基因組定序(Whole genome sequencing)探討粗首馬口鱲南北族群的高度分化是否有天擇參與，並調查近期的河川雜交狀況。此研究蒐集了臺灣西部從瑪鋉溪至港口溪總共48個樣本，定序結果為86.79%的平均覆蓋率以及10.79X的平均深度。 PCA、演化樹以及ADMIXTURE的結果與過去的研究一致。以高屏溪為界分為兩個族群，北部族群可以再分為兩個小族群，分別為苗栗中港溪以北的北部族群與介於中港溪及高屏溪之間的中部族群。高屏溪以南的河川存在許多雜交個體，而高屏溪以北則沒有檢測到任何雜交個體；粒線體與核基因的演化樹不匹配也應證了雜交的現狀。透過族群間的固定SNP （Fixed SNP）以及F3 Statistic，確認到高屏溪、枋山溪、楓港溪、四重溪以及港口溪含有雜交的基因型，高屏溪的個體則屬於對南部族群的多次回交族群，而枋山溪、楓港溪、四重溪以及港口溪則屬於F2或是中部族群的多次回交的族群。所以南北族群間還未演化出完全的生殖隔離機制。 在核基因與粒線體的演化樹上分別計算出0.47%與4.67%的遺傳距離（Genetic distance），結合南部族群不論在核基因的π值都是三個族群中的最低值，還有粒線體基因組在南北族群間最近共祖時間的高估（226萬年）。代表粒線體基因組可能受到基因漂變（Genetic drift）的影響而加速的分化。 此研究使用了FST以及族群間核苷酸多樣性(π)比率預測以高屏溪為界南北族群的候選天擇基因，檢測到Mammalian target of rapamycin (mTOR)以及Thyroid hormone receptor beta (thrb)，它們分別在斑馬魚(Danio rerio)以及食藻鱂(Cyprinodon nevadensis amargosae)上被證實參與溫度調節反應。另外南部族群中還檢測到了顯著的Thyroid hormone signaling pathway （ko04919），過去的研究顯示側線鱗數與甲狀腺素有關，而且在臺灣鬚鱲身上也發現了側線鱗與河川溫度的負相關關係。表示南北分化可能與河川溫度適應有關。

Opsariichthys pachycephalus, a primary freshwater fish species belonging to the family Xenocyprididae, is mainly distributed in rivers of western Taiwan. Based on mitochondrial DNA (mtDNA) and allozyme markers, populations can be divided into two group , northern and southern, using the Kaoping River as the boundary. Previous studies using the cytb gene have confirmed that individuals from north of the Kaoping River were introduced into rivers in the south. However, there is currently a lack of population studies based on nuclear genomic data. In this study, we applied whole-genome sequencing (WGS) to investigate whether the pronounced differentiation between the northern and southern populations of O. pachycephalus is shaped by natural selection, and to assess recent hybridization events across rivers. A total of 48 individuals were collected from rivers across western Taiwan, ranging from the Masu River to the Gangkou River. The sequencing yielded an average coverage of 86.79% and a mean depth of 10.79×. Principal Component Analysis (PCA), phylogenetic trees, and ADMIXTURE results were consistent with previous findings, identifying two major genetic groups divided by the Kaoping River. The northern group can be further subdivided into a northern subgroup (north of the Jhonggang River) and a central subgroup (between the Jhonggang and Kaoping Rivers). In contrast, many hybrid individuals were detected in rivers south of the Kaoping River, while no hybrids were found in the north. The incongruence between mitochondrial and nuclear phylogenies further supports the presence of hybridization. Through analysis of fixed SNPs and the f3 statistic, hybrid genotypes were confirmed in the Kaoping, Fangshan, Fenggang, Sichongxi, and Gangkou Rivers. Individuals from the Kaoping River were identified as multi-generation backcrosses to the southern population, while those from the other southern rivers were either F2 hybrids or backcrosses involving the central subgroup. These findings suggest that complete reproductive isolation between the northern and southern populations has not yet evolved. Genetic distances calculated from nuclear and mitochondrial phylogenies were 0.47% and 4.67%, respectively. Moreover, the southern group exhibited the lowest nucleotide diversity (π) among the three identified subgroups. In combination with an overestimated mitochondrial time to most recent common ancestor (TMRCA) between north and south populations (2.26 million years), these results suggest that mitochondrial divergence may have been accelerated by genetic drift. We further used FST and inter-population nucleotide diversity ratios (π ratios) to identify candidate genes under selection between the northern and southern populations. Notably, genes such as Mammalian target of rapamycin (mTOR) and Thyroid hormone receptor beta (thrb), both previously implicated in thermal adaptation in Danio rerio and Cyprinodon nevadensis amargosae—were identified. Additionally, the southern population showed significant enrichment of the thyroid hormone signaling pathway (ko04919). Previous studies have associated lateral line scale count with thyroid hormone levels, and in Candidia barbatus, a negative correlation has been found between scale count and river temperature. These findings suggest that the observed north–south genetic divergence may be associated with adaptation to local thermal environments.